MolNFT v1 · #104525 · protein
Crystal structure of apo KSHA5 and KSHA1 in complex with 1,4-30Q-CoA from R. rhodochrous
4QDF · 3-ketosteroid 9ALPHA-hydroxylase oxygenase: “Crystal structure of apo KSHA5 and KSHA1 in complex with 1,4-30Q-CoA from R. rhodochrous”. X-ray diffraction, 4 ligands (FES, 30Q, FE2), 12 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 4QDF
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketosteroid 9ALPHA-hydroxylase oxygenase
- UniProt
- F1CMY8, F1CMX0
- Ligands
- FES, 30Q, FE2, PO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-ketosteroid 9ALPHA-hydroxylase oxygenase | protein | 360 | 23% helix, 36% strand | F1CMY8 |
| B | 3-ketosteroid 9ALPHA-hydroxylase oxygenase | protein | 357 | 24% helix, 36% strand | F1CMX0 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
- 30Q · S-[2-(propanoylamino)ethyl] (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-6,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-17-yl]propanethioate (non-preferred name) · ligand · chains B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.78 | 0.88 | 37 | 30Q |
| 2 | 80 | 0.76 | 0.98 | 24 | FE2 |
| 3 | 205 | 0.50 | 0.76 | 25 | empty |
| 4 | 194 | 0.49 | 0.76 | 26 | empty |
| 5 | 108 | 0.48 | 0.80 | 22 | empty |
Compared structures
- 4QDF · Crystal structure of apo KshA5 and KshA1 in complex with 1,4-30Q-CoA from R. rhodochrous · the same entry in another collection · chain A against A, TM-score 1.00
- F1CMY8 · AlphaFold monomer V2.0 prediction for 3-ketosteroid-9-alpha- monooxygenase, oxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- F1CMX0 · AlphaFold monomer V2.0 prediction for 3-ketosteroid-9-alpha- monooxygenase, oxygenase… · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F1CMY8
- Every structure of UniProt F1CMX0
- Elsewhere: RCSB PDB 4QDF · PDBe 4QDF · UniProt F1CMY8 · UniProt F1CMX0
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